{"id":"https://openalex.org/W2417769830","doi":"https://doi.org/10.1109/tcbb.2015.2480056","title":"A Framework for Identifying Genotypic Information from Clinical Records: Exploiting Integrated Ontology Structures to Transfer Annotations between ICD Codes and Gene Ontologies","display_name":"A Framework for Identifying Genotypic Information from Clinical Records: Exploiting Integrated Ontology Structures to Transfer Annotations between ICD Codes and Gene Ontologies","publication_year":2015,"publication_date":"2015-09-18","ids":{"openalex":"https://openalex.org/W2417769830","doi":"https://doi.org/10.1109/tcbb.2015.2480056","mag":"2417769830","pmid":"https://pubmed.ncbi.nlm.nih.gov/26394433"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2015.2480056","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2480056","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019385227","display_name":"Seyedsasan Hashemikhabir","orcid":null},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Seyedsasan Hashemikhabir","raw_affiliation_strings":["Department of Biohealth Informatics, Indiana University-Purdue University, Indianapolis, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biohealth Informatics, Indiana University-Purdue University, Indianapolis, IN","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064654566","display_name":"Ran Xia","orcid":null},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ran Xia","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University, Columbus, OH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University, Columbus, OH","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105231932","display_name":"Yang Xiang","orcid":"https://orcid.org/0009-0001-7401-9519"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Xiang","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University, Columbus, OH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University, Columbus, OH","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066167699","display_name":"Sarath Chandra Janga","orcid":"https://orcid.org/0000-0001-7351-6268"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarath Chandra Janga","raw_affiliation_strings":["Department of Biohealth Informatics, Indiana University-Purdue University, Indianapolis, IN"],"raw_orcid":"https://orcid.org/0000-0001-7351-6268","affiliations":[{"raw_affiliation_string":"Department of Biohealth Informatics, Indiana University-Purdue University, Indianapolis, IN","institution_ids":["https://openalex.org/I55769427"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1378,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.55948281,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"15","issue":"4","first_page":"1259","last_page":"1269"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9951000213623047,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9940999746322632,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.7135328054428101},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.6206153035163879},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6129207611083984},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5209901928901672},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.510321319103241},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.47810882329940796},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.43911564350128174},{"id":"https://openalex.org/keywords/health-records","display_name":"Health records","score":0.4366839826107025},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4055922031402588},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19042804837226868},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1310437023639679},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09544166922569275},{"id":"https://openalex.org/keywords/health-care","display_name":"Health care","score":0.08870458602905273},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07724559307098389}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7135328054428101},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.6206153035163879},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6129207611083984},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5209901928901672},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.510321319103241},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.47810882329940796},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.43911564350128174},{"id":"https://openalex.org/C3019952477","wikidata":"https://www.wikidata.org/wiki/Q1324077","display_name":"Health records","level":3,"score":0.4366839826107025},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4055922031402588},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19042804837226868},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1310437023639679},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09544166922569275},{"id":"https://openalex.org/C160735492","wikidata":"https://www.wikidata.org/wiki/Q31207","display_name":"Health care","level":2,"score":0.08870458602905273},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07724559307098389},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C50522688","wikidata":"https://www.wikidata.org/wiki/Q189833","display_name":"Economic growth","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D038801","descriptor_name":"International Classification of Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038801","descriptor_name":"International Classification of Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038801","descriptor_name":"International Classification of Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbb.2015.2480056","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2480056","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26394433","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26394433","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:scholarworks.indianapolis.iu.edu:1805/13015","is_oa":false,"landing_page_url":"https://hdl.handle.net/1805/13015","pdf_url":null,"source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Author","raw_type":"Article"},{"id":"pmh:oai:scholarworks.iupui.edu:1805/13015","is_oa":false,"landing_page_url":"http://hdl.handle.net/1805/13015","pdf_url":null,"source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Author","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.47999998927116394}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W65486233","https://openalex.org/W83970946","https://openalex.org/W166302795","https://openalex.org/W175655252","https://openalex.org/W1506203134","https://openalex.org/W1550258693","https://openalex.org/W1558508164","https://openalex.org/W1929126584","https://openalex.org/W1972159638","https://openalex.org/W1979609280","https://openalex.org/W1987399111","https://openalex.org/W1989894867","https://openalex.org/W1994924587","https://openalex.org/W2022427321","https://openalex.org/W2029964044","https://openalex.org/W2052938577","https://openalex.org/W2053604224","https://openalex.org/W2054100908","https://openalex.org/W2069194720","https://openalex.org/W2078383357","https://openalex.org/W2088316091","https://openalex.org/W2106108881","https://openalex.org/W2117446594","https://openalex.org/W2117856677","https://openalex.org/W2124649657","https://openalex.org/W2125149214","https://openalex.org/W2126840542","https://openalex.org/W2135172365","https://openalex.org/W2143962926","https://openalex.org/W2146089916","https://openalex.org/W2146777736","https://openalex.org/W2148499186","https://openalex.org/W2148572968","https://openalex.org/W2149160008","https://openalex.org/W2149963380","https://openalex.org/W2155321856","https://openalex.org/W2161549461","https://openalex.org/W2168369566","https://openalex.org/W2359457515","https://openalex.org/W2889831412","https://openalex.org/W4285719527","https://openalex.org/W6602713915","https://openalex.org/W6603409865","https://openalex.org/W6630118243","https://openalex.org/W6632766574","https://openalex.org/W6633504300","https://openalex.org/W6707285555"],"related_works":["https://openalex.org/W2085384747","https://openalex.org/W2106071040","https://openalex.org/W2003333417","https://openalex.org/W2088166309","https://openalex.org/W4312133475","https://openalex.org/W4238976562","https://openalex.org/W2276587472","https://openalex.org/W4248323080","https://openalex.org/W2615795876","https://openalex.org/W2049612369"],"abstract_inverted_index":{"Although":[0],"some":[1],"methods":[2],"are":[3],"proposed":[4],"for":[5,26,79],"automatic":[6],"ontology":[7],"generation,":[8],"none":[9],"of":[10,15,30,40,54,83,92,97],"them":[11,102,124],"address":[12],"the":[13,55,60,90,116],"issue":[14],"integrating":[16,27],"large-scale":[17],"heterogeneous":[18],"biomedical":[19],"ontologies.":[20],"We":[21,74,142],"propose":[22],"a":[23,76,80,139],"novel":[24],"approach":[25,51],"various":[28],"types":[29],"ontologies":[31],"efficiently":[32],"and":[33,47,85,88,110,149],"apply":[34],"it":[35],"to":[36,58,120],"integrate":[37],"International":[38],"Classification":[39],"Diseases,":[41],"Ninth":[42],"Revision,":[43],"Clinical":[44],"Modification":[45],"(ICD9CM),":[46],"Gene":[48],"Ontologies.":[49],"This":[50],"is":[52],"one":[53],"early":[56],"attempts":[57],"quantify":[59],"associations":[61,119,133,148],"among":[62],"clinical":[63],"terms":[64,96],"(e.g.,":[65],"ICD9":[66,86,118],"codes)":[67],"based":[68],"on":[69],"their":[70],"corresponding":[71],"genomic":[72],"relationships.":[73],"reconstructed":[75],"merged":[77],"tree":[78,94],"partial":[81],"set":[82],"GO":[84],"codes":[87],"measured":[89],"performance":[91],"this":[93],"in":[95],"associations'":[98],"relevance":[99],"by":[100,135],"comparing":[101],"with":[103],"two":[104],"well-known":[105],"disease-gene":[106],"datasets":[107],"(i.e.,":[108],"MalaCards":[109],"Disease":[111],"Ontology).":[112],"Furthermore,":[113],"we":[114],"compared":[115],"genomic-based":[117],"temporal":[121],"relationships":[122],"between":[123],"from":[125,153],"electronic":[126],"health":[127],"records.":[128],"Our":[129],"analysis":[130],"shows":[131],"promising":[132,151],"supported":[134],"both":[136],"comparisons":[137],"suggesting":[138],"high":[140],"reliability.":[141],"also":[143],"manually":[144],"analyzed":[145],"several":[146],"significant":[147],"found":[150],"support":[152],"literature.":[154]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
